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Most movies are fairly simplistically formulations between one good protagonist and one bad antagonist.

Part of the greatness of the Star Trek franchise is that its plots were always multi-dimensional even from the original.

What child wants to continue playing checkers after learning how to play chess?

Another greatness of Star Trek is that it was really roughly modeled upon our own world.

In the TV series, the Federation represents America as it continues to do in the current movie. 

(Actually, and not to get side-tracked, but Star Trek was the first TV series to  promote a One-World diverse United Nations utopia, as Chekov represented all Slavic peoples, Uhura represented all African people, Scotty represented all of the British Empire, Sulu represented all Asians, Captain Kirk represented the best and brightest of America of course, and who knows whom Spock represented.  Sorry Latinos, neither the TV series nor this movie was that much into you!  And the original TV series also left out all of the 1 billion Muslims, centered in the Middle East, which we will see will be rectified in the new movie.)

Star Trek also represented the political ideologies of the Cold War with the American Federation representing the free world, the Romulans representing the Cold War era Russians and the Klingons representing the Cold War era Chinese.

Well obviously there is no longer a cold war, so the current movie had to make modern day substitutes to remain relevant

The mold I see being cast in the latest movie is that the Klingons now represent Middle Eastern Muslims in their part of the Earthly universe, with all our wars and threats of war against them; while, the Botany Bay clan of super humans under the Wrath of Khan represents the Jews -- dangerously living in total freedom among unsuspecting Christians and plotting any and all means of taking absolute power and authority into their own hands.

The main plot of Into Darkness revolves around Kirk having to decide if others are an eminent threat to society or having to decide if they are just well-meaning protectors of Earth.

Kirk surely knows his traditional and clear cut enemy, the Klingons, but he quickly finds himself having to determine if another secret and sly enemy exists within his own ranks, one who knows far more and one who is far more capable of doing damage than any Klingon warship could hope to achieve.

To complicate matters more, Kirk finds himself confronted with not just one critical decision about friend or foe, but two closely interrelated ones whom may or may not be designing dastardly deeds together.

The Judeo-Khan has surfaced and he is clearly the leader of "The Chosen People" of super humans, with Khan willing to do ANYTHING to insure the survival of his evil clan of Chosen People.

His is a super human race, not blessed by God, but blessed by a genetically superior intellect and genetically superior talents, coupled with an intense maniacal desire to rule over and subjugate all "inferiors".

We first learn of this Judeo-Khan as he is systematically destroying Star Fleet Command from within. How does this mysterious Star Fleet operative know so much about Star Fleet Command?

Luckily Captain Kirk thwarts his efforts and Khan escapes to a part of Middle Eastern Klingon space, uninhabited by Muslim Klingons, which in reality can only be Jerusalem.

Kirk is dispatched by Admiral Marcus to kill Khan on sight.  A suicidal mission as Admiral Marcus has also seen to it that Captain Kirk's warp drive is disabled upon arrival in Muslim Klingon space.

Is the disabling of Kirk's ship a shrewd double check to insure that should Khan somehow utilize his superior intellect to take control of Kirk's Star Ship, then he will not have a functioning Star Ship? 

Or is Admiral Marcus just plain pure evil and wants all evidence of his machinations buried with Kirk, knowingly sacrificing Kirk when the Muslim Klingons discover Kirk's presence, and conveniently thereby setting off the war of the universe Admiral Marcus so badly desires?

Is Captain Kirk being set up as a modern day U.S.S Maine?  A small sacrifice for the greater good, for once discovered, an act of war will surely exist between the Federation and the Klingons as was the case when the U.S.S. Maine exploded in Havana's harbor. Is such a fate as Admiral Marcus is clearly wishing for so he can use the new super weapons developed by Khan to destroy the threat of the Klingons forever?

Was Admiral Marcus using Khan or was Khan using Admiral Marcus?

The parallels to our world are obvious.

American Federation leaders giving our latest military technology to Khan's chosen people in Israel so they can "improve upon it", with plenty of Khan's operatives securely situated in key positions in American Federation command and control.

American Federation leaders saying for our national security that we need to have war against the Iranian Klingons, whom by the way, only threaten Khan's Israel.

Into Darkness shows the blind and ignorant trust the Federation Admiral has that the Judeo-Khan would help the Federation, without figuring out a way of helping himself to the spoils. His people are held as hostage, yet Admiral Marcus hand delivers them all to Khan embedded in 72 prototype photon torpedoes. Khan would recognize the number 72 as being the exact number of people in his clan.

Judeo-Khan would not allow such a Holocaust of his Chosen People and immediately  surrenders himself to Kirk.

This is exactly where the foolish American Federation "useful idiot" commander has seriously jeopardized the entire American Federation to utter destruction.

The Judeo-Khan knows the inner workings of the American Federation far better than anyone in the American Federation does, and save the bold heroics of Captain Kirk, the American Federation would have become a Judeo-Khan-led Communist hellhole.

The story line is that there are very few Captain Kirks who can detect real enemies living among us, and once again, the movie sadly parallels reality.